Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024640.1 Corchorus olitorius cultivar O-4 contig24673, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 37080
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:1755 original size:6 final size:6
Alignment explanation
Indices: 1741--1777 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
1731 AGGCTGCACT
* *
1741 ACAATC ACCATC ACCATC ACAATC ACAATC ACAATC A
1 ACAATC ACAATC ACAATC ACAATC ACAATC ACAATC A
1778 TCCGTTAACG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.46, C:0.38, G:0.00, T:0.16
Consensus pattern (6 bp):
ACAATC
Found at i:1933 original size:39 final size:38
Alignment explanation
Indices: 1807--1953 Score: 217
Period size: 38 Copynumber: 3.9 Consensus size: 38
1797 TCGAGTCTAG
1807 CCAACAG-TTAACCCCCTGAGGCACGGGTCCACTCTTA
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
1844 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
* * *
1882 CCAACAGTTTAACCCCCTGTGGTATGGGTCCACTCTTTA
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTC-TTA
* **
1921 CCATCAGTTTAA-CCCCTGAGGTTCGGGTCCACT
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACT
1954 ATGCACAGCA
Statistics
Matches: 101, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
37 7 0.07
38 80 0.79
39 14 0.14
ACGTcount: A:0.22, C:0.35, G:0.19, T:0.24
Consensus pattern (38 bp):
CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
Found at i:10156 original size:1 final size:1
Alignment explanation
Indices: 10150--10182 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
10140 GGTAAAAGTT
10150 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
10183 TCTTCTCAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:15738 original size:15 final size:15
Alignment explanation
Indices: 15715--15744 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
15705 TACGGTTGAA
*
15715 ATATTGTGTATCGTG
1 ATATCGTGTATCGTG
15730 ATATCGTGTATCGTG
1 ATATCGTGTATCGTG
15745 GCAGCCTGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.10, G:0.27, T:0.43
Consensus pattern (15 bp):
ATATCGTGTATCGTG
Found at i:17564 original size:24 final size:24
Alignment explanation
Indices: 17537--17582 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
17527 GTCATTAATG
17537 ACTTGGTAAGTCTTCATGGGAATT
1 ACTTGGTAAGTCTTCATGGGAATT
17561 ACTTGGTAAGTCTTCATGGGAA
1 ACTTGGTAAGTCTTCATGGGAA
17583 ATTTAAAGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.35
Consensus pattern (24 bp):
ACTTGGTAAGTCTTCATGGGAATT
Found at i:21914 original size:21 final size:21
Alignment explanation
Indices: 21888--21946 Score: 68
Period size: 19 Copynumber: 2.9 Consensus size: 21
21878 TAAAAATTCT
*
21888 CATTACACTAAAAAATGATAC
1 CATTACACCAAAAAATGATAC
* *
21909 CATTACACCAAATAA-GA-AT
1 CATTACACCAAAAAATGATAC
*
21928 CATTACACCAAAAATTGAT
1 CATTACACCAAAAAATGAT
21947 TTTTTTCACA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
19 14 0.45
20 4 0.13
21 13 0.42
ACGTcount: A:0.51, C:0.20, G:0.05, T:0.24
Consensus pattern (21 bp):
CATTACACCAAAAAATGATAC
Found at i:29858 original size:37 final size:37
Alignment explanation
Indices: 29808--29878 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
29798 CCAATTAGGG
29808 TTAGTAAAAAAAATTAAAATTGTTATTGTTCATGGGA
1 TTAGTAAAAAAAATTAAAATTGTTATTGTTCATGGGA
29845 TTAGTAAAAAAAATTAAAATTGTTATTGTTCATG
1 TTAGTAAAAAAAATTAAAATTGTTATTGTTCATG
29879 AATGAGTGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.44, C:0.03, G:0.14, T:0.39
Consensus pattern (37 bp):
TTAGTAAAAAAAATTAAAATTGTTATTGTTCATGGGA
Found at i:30958 original size:45 final size:45
Alignment explanation
Indices: 30894--30988 Score: 154
Period size: 45 Copynumber: 2.1 Consensus size: 45
30884 CCAACTATAA
* *
30894 GAAGAAGATGTTGCATGATTTGACTACAGTGACAACAATTGCATT
1 GAAGAAGATGTTGCATGATTCGACTACAGAGACAACAATTGCATT
* *
30939 GAAGAAGATGTTGCATGATTCGATTACAGAGGCAACAATTGCATT
1 GAAGAAGATGTTGCATGATTCGACTACAGAGACAACAATTGCATT
30984 GAAGA
1 GAAGA
30989 TTCTGGCGAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.26
Consensus pattern (45 bp):
GAAGAAGATGTTGCATGATTCGACTACAGAGACAACAATTGCATT
Found at i:34624 original size:21 final size:20
Alignment explanation
Indices: 34598--34643 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
34588 ATACCAGTCG
*
34598 AATATGGAAGTATTTCCATAC
1 AATATGGAA-TACTTCCATAC
*
34619 AATATGTAATACTTCCATAC
1 AATATGGAATACTTCCATAC
34639 AATAT
1 AATAT
34644 TTGTTGGTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.41, C:0.15, G:0.09, T:0.35
Consensus pattern (20 bp):
AATATGGAATACTTCCATAC
Found at i:35785 original size:29 final size:30
Alignment explanation
Indices: 35727--35787 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
35717 GTTCTATTGA
* *
35727 ATGTATACATATAAATTATTCAATTTTATT
1 ATGTATAAATATAAATTATTCAATTATATT
*
35757 ATGTATAAATAT-AATTATTTAATTATATT
1 ATGTATAAATATAAATTATTCAATTATATT
35786 AT
1 AT
35788 ATTATTTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 17 0.61
30 11 0.39
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (30 bp):
ATGTATAAATATAAATTATTCAATTATATT
Found at i:36939 original size:55 final size:55
Alignment explanation
Indices: 36861--36971 Score: 204
Period size: 55 Copynumber: 2.0 Consensus size: 55
36851 GAATCCTAAA
*
36861 AACCCCTCTTTTTAAGATCATCATAATTTATTTTACACCCTTTACACTTTAAAAC
1 AACCCCTCTTTTTAAGATCATCATAATTTAATTTACACCCTTTACACTTTAAAAC
*
36916 AACCCCTCTTTTTAAGATCATCATAATTTAATTTACACCCTTTATACTTTAAAAC
1 AACCCCTCTTTTTAAGATCATCATAATTTAATTTACACCCTTTACACTTTAAAAC
36971 A
1 A
36972 TAAAACATTT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.34, C:0.24, G:0.02, T:0.40
Consensus pattern (55 bp):
AACCCCTCTTTTTAAGATCATCATAATTTAATTTACACCCTTTACACTTTAAAAC
Found at i:36983 original size:55 final size:55
Alignment explanation
Indices: 36869--36983 Score: 160
Period size: 55 Copynumber: 2.1 Consensus size: 55
36859 AAAACCCCTC
* *** *
36869 TTTTTAAGATCATCATAATTTATTTTACACCCTTTACACTTTAAAACAACCCCTC
1 TTTTTAAGATCATCATAATTTAATTTACACCCTTTACACTTTAAAACAAAAACTA
*
36924 TTTTTAAGATCATCATAATTTAATTTACACCCTTTATACTTTAAAACATAAAAC-A
1 TTTTTAAGATCATCATAATTTAATTTACACCCTTTACACTTTAAAACA-AAAACTA
36979 TTTTT
1 TTTTT
36984 CTAGTTGGGC
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
55 51 0.96
56 2 0.04
ACGTcount: A:0.36, C:0.20, G:0.02, T:0.43
Consensus pattern (55 bp):
TTTTTAAGATCATCATAATTTAATTTACACCCTTTACACTTTAAAACAAAAACTA
Done.